aslozada / kanon

Program to compute chirality indices and assess molecular symmetry

Program to compute chirality indices and assess molecular symmetry

This is the official repository of the kanon program developed by Asdrubal Lozada-Blanco in the Laboratory of Theoretical Chemistry (Federal University of São Carlos - Brazil)

Installation

Building from source

To build kanon from source code you need to have:

• a Fortran compiler
• build systems: make or fpm
• fpm version 0.2.0 or newer

Building with make

cp app/kanon.f90 src/
cp Makefile src/
cd src/
make clean
make
make clean

Building with fpm

fpm build

How to use kanon?

kanon uses a XYZFile as input

natom
comment
label1 xcoor1 ycoord1 zcoord1
label2 xcoor2 ycoord2 zcoord2
...

Examples

3
Water H2O.xyz
O     0.000000     0.000000     0.000000
H     0.000000     0.000000     0.947000
H     0.895670     0.000000    -0.316663

kanon --pattern H2O.xyz

---------------------------------------------------------------------------------
Cartesian coordinates input file: H2O.xyz
Number atoms:     3
 O    0.00000   0.00000   0.00000
 H    0.00000   0.00000   0.94700
 H    0.89567   0.00000  -0.31666

-----------------------------------------------------------------------------
Diameter of molecule:    1.54889 ang.
--------------------------------------------------------------------------------
Center of masses
   0.05011   0.00000   0.03527
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Principal moments of inertia
     Ia           Ib           Ic
   0.53688      1.20907      1.74595
--------------------------------------------------------------------------------
Inertia axis
   0.00000   0.81430  -0.58045
   1.00000   0.00000   0.00000
   0.00000   0.58045   0.81430
--------------------------------------------------------------------------------
Symmetry elements. Tolerance:    0.05000
--------------------------------------------------------------------------------

kanon --single <H2O>.xyz

-----------------------------------------------------------------------------
Diameter of molecule:    1.54889 ang.
-----------------------------------------------------------------------------
Center of masses:    0.05011   0.00000   0.03527
------------------------------------------------------------------------------
Moments of inertia:       1.74595      1.20907      0.53688
Eigenvectors
     0.000     0.814    -0.580
     1.000     0.000     0.000
     0.000     0.580     0.814
---------------------------------------------------------------------------------
Symmetrical matrix in Diamond`s method to optimal rotation: B
---------------------------------------------------------------------------------
     0.000     0.000     0.000     0.000
     0.000     3.353    -0.000    -0.000
     0.000    -0.000     2.399    -0.001
     0.000    -0.000    -0.001     0.954
---------------------------------------------------------------------------------
 Eigenvalues   -   Eigenvectors
---------------------------------------------------------------------------------
     0.954     0.000     0.000     0.000     1.000
     0.000     1.000     0.000     0.000     0.000
     3.353     0.000     1.000    -0.000    -0.000
     2.399     0.000     0.000     1.000    -0.000
--------------------------------------------------------------------------------
Check files: Pattern.xyz / Rotate_image.xyz
---------------------------------------------------------------------------------
Root-mean-square deviation
RMSD:   0.00000000
--------------------------------------------------------------------------------
Hausdorff-derived chirality Index
CHI:    0.00000000
--------------------------------------------------------------------------------

Comparing an object with any image

kanon --pattern <object>.xyz --image <image>.xyz

Delaunay triangulation of surfaces

kanon --pattern <file>.xyz --delaunay <output_grid>.dat

output_grid.dat

GRID       1286
REF  6 2 1
            6         2         1
            6         3         2
            4        70         3
            4        69        70
           70        69        74
           71        70        74
...

With openmp

export OMP_NUM_THREADS=#

Example: Hausdorff Chirality Measure for biphenyl

Grid's effects

Electron density: Isovalue 0.05